[Biococoa-dev] More goodies!!
charles.parnot at gmail.com
Mon Mar 6 14:54:40 EST 2006
> Hi Charles,
> If I get you right, you would prefer option 3, so you'd move the
> "AlexCode" to a separate folder in the trunk?
> I'm a bit confused... sorry
Well, actually, it seems like I do, though I did not really realize :-)
My point is simply: Alex's code is being used in 1-3 "stable"
applications, and will thus be tested and used quite a lot. Such code
is very valuable and should be included "as is" in the repository. I
realize now that you want to avoid "extra" code outside of the
BioCocoa stuff. So, at least, BioCocoa 1.7 could be included.
Including the other "goodies" may or may not make sense, and may or
may not make things more confusing. However, maybe restricting it to
a particular subdir in the Tags directory is still OK, as this is the
place for "frozen" items. Starting branches with these is probably a
very bad idea, and I would actually not include a BioCocoa/Branches/
Goodies directory, shame on me!
All of this also depends how you can bundle things. If the new
BCReader integrates well with BioCocoa 1.6, then we should definitely
make a BioCocoa 1.7 with it. Regarding the other extras, we could
bundle them with BioCocoa 1.7, or keep them separate (Goodies), or
not include them. Again, if they can be bundled easily and
transparently with it, then we should do it, so the good code is
there on the repository.
Alex, what do you think? In your email, you proposed:
> Also, I think its time to update the BioCocoa website to represent
> this all.
> It should give a general introduction of who we are and what we aim.
> It should describe the current stable releases (BioCocoa 1.6 +
> "BCAppkitStandalone", with links to download etc
> It should describe our current plans on developing BioCocoa 2.0 ->
> give some ideaof what we want and info on how to join, access the
> svn server etc.
but did you mean to have BioCocoa 1.6 + "BCAppkitStandalone"
available on the svn server?
In the end, don't worry too much about what I say, Peter: do what you
think is best. Anyway, we can always decide to add stuff later, and
start with some minimal layout for now.
> On 06 Mar 2006, at 18:49, Charles Parnot wrote:
>> I don't think we need 2 repositories. Subversion is very
>> convenient for branches and tags. I think Alex's final code should
>> be included "as is" in the current svn directory, as a side
>> project of BioCocoa, because this is usable-right-now tested code,
>> just like BioCocoa 1.6 is. I would do the following structure in
>> the repository, something close to the usual "recommanded" layout:
>> ......[Checkout of the latest CVS repository]
>> ......BioCocoa 1.6 <-- BCReader from Peter
>> ......BioCocoa 1.7 <-- BCReader from Alex
>> .........EntrezController 1.0 <--- From Alex
>> .........KDTextView 1.0 <-- From Koen
>> .........KDTextView 1.1 <-- From Alex
>> The "Goodies" directory could be named something else, like
>> "Subprojects" or whatever you like, and might alternatively be
>> moved to the root (under BioCocoa), and have its own Trunk, Tags
>> and Branches.
>> The "Branches" directory is empty right now, but might soon have a
>> "BioCocoa 1.x" branch if we want to fix bugs / add features on the
>> 1.7 version, and/or have a "Goodies/KDTextView 1.x" branch for the
>> same reasons. Of course, the code for these should be merged in
>> the BioCocoa Trunk as soon as possible too, and we probably don't
>> want to generate too much code on the 1.x versions.
>> Let's take advantage of super-easy management of Tags and Branches
>> with Subversion... Just my 2 cents!
>> On Mar 6, 2006, at 4:33 AM, Peter Schols wrote:
>>> Hi Alex and other listers,
>>> This BCAppkitTest works great and it will be a great addition to
>>> Over the weekend, I have worked with the - very helpful - people
>>> at Bioinformatics.org to solve my login problems (it turned out
>>> to be a proxy issue that was caused by a bug on their end, they
>>> have been able to fix it).
>>> As a result, I am totally ready to start the subversion
>>> repository and do the initial import.
>>> The main question I have now is: how should we organise the
>>> repository and the BioCocoa website? There are several scenarios:
>>> 1. Checkout the latest version of the BioCocoa framework from CVS
>>> and use that as the initial import for SVN. Make the BCAppkitTest
>>> available as a download on our website (both source and compiled
>>> app) but wait to put it in the repository until it's adapted to
>>> use the classes in our own framework.
>>> 2. Checkout the latest version of the BioCocoa framework from CVS
>>> and use that as the initial import for SVN. Make a second
>>> repository (I think this is possible @ bioinformatics.org) and
>>> put BCAppkitTest in there.
>>> 3. Checkout the latest version of the BioCocoa framework from
>>> CVS, add the BCAppkitTest somewhere in the hierarchy of that same
>>> BioCocoa folder and check this hybrid framework in to one
>>> I think I'd prefer solution number 1 (or 2) because
>>> - it seems a bit weird to have part of a framework that does not
>>> use the base classes available in the rest of the framework
>>> - it might confuse users of the framework
>>> - we should aim to integrate BCAppkitTest into BioCocoa asap,
>>> this won't be a huge undertaking
>>> Please let me know your preference and I would be glad to create
>>> the Subversion repository and send instructions on using it. I'd
>>> also be glad to update the website and make the BCAppkitTest
>>> On 06 Mar 2006, at 11:08, Alexander Griekspoor wrote:
>>>> Hi guys,
>>>> With EnzymeX3 now in beta testing phase it's time to share the
>>>> I've thrown together a very simple demo app showing the three
>>>> goodies I would like to donate back to the BioCocoa project:
>>>> - BCReader, the standalone BCReader classes for sequence file
>>>> IO (original version Peter Schols)
>>>> - EntrezController, a controller plus view for browsing and
>>>> fetching NCBI's Entrez Database
>>>> - KDTextView+, a custom NSTextView for displaying biological
>>>> sequences (original version Koen van der Drift)
>>>> Download and enjoy at: http://www.mekentosj.com/biococoa/
>>>> Of course all feedback and bug reports are welcome (or not
>>>> depending on how you interpret this sentence ;-)
>>>> Also, coming back to Koen's remark. There are a few things I/we
>>>> could do.
>>>> First, it would be nice if it had these views mentioned as
>>>> available on the website and the code given a place on the svn
>>>> Second, we could perhaps post a small announcement (few lines)
>>>> on cocoa-dev to notify other cocoa developers, also letting them
>>>> know about BioCocoa again.
>>>> Finally, we could compose a little message to MacResearch
>>>> describing the BioCocoa project and also the availability of
>>>> this code.
>>>> Alternatively, I can inform them about it when we release the
>>>> EnzymeX final version. I believe Tom spoke a few times with the
>>>> guys behind MacResearch, so we could inform them directly.. Let
>>>> me know what you guys think.
>>>> ** Alexander Griekspoor **
>>>> The Netherlands Cancer Institute
>>>> Department of Tumorbiology (H4)
>>>> Plesmanlaan 121, 1066 CX, Amsterdam
>>>> Tel: + 31 20 - 512 2023
>>>> Fax: + 31 20 - 512 2029
>>>> AIM: mekentosj at mac.com
>>>> E-mail: a.griekspoor at nki.nl
>>>> Web: http://www.mekentosj.com
>>>> 4Peaks - For Peaks, Four Peaks.
>>>> 2004 Winner of the Apple Design Awards
>>>> Best Mac OS X Student Product
>>>> Biococoa-dev mailing list
>>>> Biococoa-dev at bioinformatics.org
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>> Charles Parnot
>> charles.parnot at gmail.com
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